The CLIC Electronic Chemistry Journal Project
The CLIC Electronic Chemistry Journal Project
hemistry is one of the most visual and "three dimensional"
of sciences. For many generations, communication of the
subject has been rooted on the printed pages of chemical journals, with even colour
a rare event. Partially because of such limitations, the subject has evolved a complex and arcane symbolism
for its written representation. The complexities of this "chemical
nomenclature" in turn result in substantial risk of the propagation
of errors and misinterpretation of results. A refereeing system exists
to catch both errors of science and transcription errors, but the
reality is that referees have few "tools" to assist them to catch errors
on the printed page other than then own eyes and minds!
To illustrate how important this can be,
consider the antimalerial drug halofantrin. It can have two
so called chiral forms, 
known as R and S. This molecule also
has a very unusual way of
interacting with itself ("self-associating") that directly impinges on the method
used to separate these two forms (using a process known as chiral separation chromatography).
The
difference between the R and S forms and how they can be chromatographically separated can only
be understood if the chemical structure of
the molecule is considered in three
dimensions. It takes a highly
experienced and confident chemist to
translate the diagram shown here, together
with the R/S symbolic notation, into the
laboratory synthesis of a safe
pharmaceutical product.
On the printed page, all that can be shown is a two dimensional image taken
from one particular perspective view of this molecule.
However, in this view, the user
cannot rotate or inspect the molecule themselves, and obscured
aspects will be hidden.
Modern chemistry is often concerned with systems which might be one hundred times larger and more complex, and the reader may also wish to acquire say detailed toxicology or synthesis data, spectral and instrumental information, accurate three dimensional coordinates for the molecule determined from x-ray crystallography, the structures of a few dozen analogues, details of any enzymes involved in metabolic pathways, mathematical algorithms that describe the molecular properties, and theoretical models which might describe the mechanisms of its behaviour. Most importantly, the reader will also wish to acquire all this information without any risk of transcription errors, in an instantly usable form for further processing by computer.
The CLIC consortium comprises groups in three university chemistry departments (Imperial College, Leeds and Cambridge Universities) and a learned society (The Royal Society of Chemistry) whose basic aim is to create an electronic chemistry journal ("Chemical Commuinications") that will provide such information to the reader, with what might be called "semantic integrity" and accuracy of the information. We even envisage providing mechanisms for readers to comment on the individual articles, and thus to interact with the original authors. To this extent, this aim differs from some other electronic journals, where the paramount objective is to achieve what is called "page integrity" with the original printed version. Whilst semantic and page integrity are not necessarily exclusive, to achieve both requires significant extra effort in storing the basic content of the journal, and its presentation to the user. Thus the CLIC project will concentrate on developing standards for storing, transmitting, displaying and applying molecular information. Not the least task is educating the audience to actively participate in this method of information retrieval, and indeed persuading authors to contribute information in the appropriate form in the first place.
The CLIC Project also appears in the News section of this issue, with an item by David James.
Contents Page
- Electronic Libraries Programme and Project Information
News Desk - Search Ariadne - Mail - About Ariadne - Front Page